Metagenomics has enabled a greater understanding of microbial community dynamics than previously realized and now the challenge is to integrate microbial dynamics into ecological models. My lab takes an ‘omics approach mixed with classical microbiology to identify factors affecting microbial communities and how an altered microbial community will affect macro-organism health and ecosystem functioning. The key habitats are coral reefs and kelp forests. Within the kelp forest, we have started with a culturing approach that has identified novel genomes associated with the giant kelp Macrocystis pyrifera. Phenotypic assessments of these bacteria have identified increase in the microbe’s ability to tolerate copper and resist antibiotics with increasing human activities. We have tested the effects of altered microbial abundance and community composition on survival and development of M. pyrifera gametophytes. Decreasing microbial abundance enhanced M. pyrifera recruitment, increasing zoospore settlement and gametophyte development. Gametophytes reared in microbial communities sampled adjacent to the populated city showed lower survival and growth compared to gametophytes in microbial communities from a remote island. Metagenomics revealed a high abundance of phototrophic and oligotrophic microbes from the island, compared with an abundance of eutrophic microbes adjacent to the city. In addition, microbes adjacent to the city lacked genes that produce quorum signaling molecules, negatively influencing kelp spore settlement. Long term analyses of the microbial communities from the kelp forest have been initiated and we are currently investigating the microbes associated with the water column and kelp surface at two distinct depth. First, at 0.5 m depth where the water is warmer, highly oxygenated and receiving large amounts of carbon from photosynthesis and second, at 15 m depth where the water is under seasonal thermocline, colder, lower in oxygen, and can potentially be exposed to high partial pressure of carbon dioxide. Monthly sampling has revealed microbial number is lower at depth and pCO2 is higher. Metagenomic analysis of these samples is under way. Kelp feeds the ecosystem through degradation and we are currently investigating the effects of microbes on kelp degradation and subsequent nutritional value. We have shown altered microbial communities are detrimental to kelp recruitment and are identifying way of adding these data to ecosystem models.